2005/7/29, Miguel <miguel@...>:
> >> Q: Park Won-Kyu, Did you write the JmolProcessor?
> >>
> >
> > No Im not. I made a JmolProcessor for the MoniWiki (MoniWiki is a
> > MoinMoin clone based on PHP)
>=20
> OK
>=20
> Does MoniWiki have support for macros?
>
Yes. It has very similar mechanism

>> Q: Park Won-Kyu, Did you write the JmolProcessor?
>>
>
> No Im not. I made a JmolProcessor for the MoniWiki (MoniWiki is a
> MoinMoin clone based on PHP)
OK
Does MoniWiki have support for macros?
Miguel

Hi Miguel,
De: Park Won-Kyu <wkpark=40gmail.com>
>> Q: Park Won-Kyu, Did you write the JmolProcessor?
>>
>
>No Im not. I made a JmolProcessor for the MoniWiki (MoniWiki is a
>MoinMoin clone based on PHP)
Based on the comment at the bottom of http://wiki.jmol.org/JmolProcessor, =
it seems that the JmolProcessor for MoinMoin was written by Oliver
Nicolas

2005/7/29, Miguel <miguel@...>:
> >>I am interested in extending MoinMoin so that we can embed JmolApplets =
+
> controls directly into the wiki pages.
> [snip]
> >>Q: What is the JmolProcessor?
> >
> > I think it's the extension that enables embedding Jmol applets in wikis=
.
> For what I understand in http://wiki.jmol.org/JmolProcessor, there is
> already one done for MoinMoin wiki, and it is available in Jmol wiki.
>=20
> Without knowing that the JmolProcessor existed, I developed an alternate
> mechanism to support embedding Jmol into a MoinMoin wiki.
>=20
> It parallels the Jmol.js JavaScript library, and allows you to embed
> buttons, checkboxes, etc.
>=20
> I would like to get it installed on wiki.jmol.org
>=20
> Q: Oliver, are you around? Or are you away on holiday?
>=20
> Q: Park Won-Kyu, Did you write the JmolProcessor?
>
No Im not. I made a JmolProcessor for the MoniWiki (MoniWiki is a
MoinMoin clone based on PHP)
>=20
> I would like to have a discussion about the JmolProcessor, the macros
> which I have developed, and determine how we can best integrate them.
>=20
>=20
> Miguel
>=20
> -----
> Open Source Molecular Visualization
> http://www.jmol.org
> miguel@...

Bugs item #1178627, was opened at 2005-04-07 11:31
Message generated for change (Comment added) made by migueljmol
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1178627&group_id=23629
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: File Input/Output
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: esor_ekim (esor_ekim)
Assigned to: Miguel (migueljmol)
Summary: jmol-10 not happy with clm input file, although jmol-9 is OK
Initial Comment:
jmol-10 cmldiamond.cml
Warning! This version of jmol has the following features:
Last line of pdb files can be discarded if not END
PNG output is uncompressed (so save as PPM and use
pnmtopng)
PDF output has A4 boundingbox (so save as PPM and use
bmp2eps -pdf)
jmol version 10 starting...
splash_image=jar:file:/a/tcmsf1/apps/tru64/jmol/jmol-10/Jmol.jar!/org/openscience/jmol/images/Jmol_splash.jpg
using Smarter Model Adapter
(C) 2004 The Jmol Development Team
Jmol Version 10.00 2004/12/17 18:55
java.vendor:Sun Microsystems Inc.
java.version:1.4.2_06
os.name:Linux
User macros dir: /u/tcmsf1/mr349/.jmol/macros
exists: false
isDirectory: false
animationReplayMode=0
FileManager.openFile(cmldiamond.cml)
SmarterJmolAdapter:The Resolver thinks:Cml
Using JAXP/SAX XML parser.
openFile(cmldiamond.cml) 131 ms
uncaught exception: java.lang.NullPointerException:
Bspt leaf splitting error
java.lang.NullPointerException: Bspt leaf splitting error
at org.jmol.viewer.Bspt$Leaf.<init>(Bspt.java:450)
at org.jmol.viewer.Bspt$Node.<init>(Bspt.java:362)
at org.jmol.viewer.Bspt.addTuple(Bspt.java:95)
at org.jmol.viewer.Bspf.addTuple(Bspf.java:56)
at
org.jmol.viewer.Frame.initializeBspf(Frame.java:997)
at org.jmol.viewer.Frame.rebond(Frame.java:1085)
at
org.jmol.viewer.Frame.doAutobond(Frame.java:1058)
at org.jmol.viewer.Frame.<init>(Frame.java:188)
at
org.jmol.viewer.ModelManager.setClientFile(ModelManager.java:72)
at
org.jmol.viewer.Viewer.openClientFile(Viewer.java:1029)
at
org.jmol.viewer.Viewer.getOpenFileError1(Viewer.java:1002)
at
org.jmol.viewer.Viewer.getOpenFileError(Viewer.java:987)
at
org.openscience.jmol.app.Jmol.main(Jmol.java:398)
input file is uploaded.
----------------------------------------------------------------------
>Comment By: Miguel (migueljmol)
Date: 2005-07-28 13:17
Message:
Logged In: YES
user_id=1050060
When I try to load this in the current development version
of Jmol I am getting a different error.
I am getting NaN (Not A Number) values in many of hte
floating point values. It is not clear to me why this is
happening.
I suspect that there is something going on with the
coordinates of this file ... like something going to
infinity during a matrix math operation.
Q: Are you sure this file is valid CML?
Q: Can you give me any hints about the structure? Something
that may cause the matrix math to explode?
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1178627&group_id=23629

>>I am interested in extending MoinMoin so that we can embed JmolApplets =
+
controls directly into the wiki pages.
=5Bsnip=5D
>>Q: What is the JmolProcessor?
>
> I think it's the extension that enables embedding Jmol applets in wikis=
.
For what I understand in http://wiki.jmol.org/JmolProcessor, there is
already one done for MoinMoin wiki, and it is available in Jmol wiki.
Without knowing that the JmolProcessor existed, I developed an alternate
mechanism to support embedding Jmol into a MoinMoin wiki.
It parallels the Jmol.js JavaScript library, and allows you to embed
buttons, checkboxes, etc.
I would like to get it installed on wiki.jmol.org
Q: Oliver, are you around? Or are you away on holiday?
Q: Park Won-Kyu, Did you write the JmolProcessor?
I would like to have a discussion about the JmolProcessor, the macros
which I have developed, and determine how we can best integrate them.
Miguel
-----
Open Source Molecular Visualization
http://www.jmol.org
miguel=40jmol.org
-----

Bugs item #1221478, was opened at 2005-06-15 15:48
Message generated for change (Comment added) made by migueljmol
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1221478&group_id=23629
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: File Input/Output
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: dcaffrey (dcaffrey)
Assigned to: Miguel (migueljmol)
Summary: incorrect bonds
Initial Comment:
If you load pdb 1A5Z in to Jmol, the number of bonds
between cadmium and ASP 168 is incorrect.
----------------------------------------------------------------------
>Comment By: Miguel (migueljmol)
Date: 2005-07-28 12:54
Message:
Logged In: YES
user_id=1050060
Can this bug be closed?
----------------------------------------------------------------------
Comment By: Miguel (migueljmol)
Date: 2005-06-15 21:53
Message:
Logged In: YES
user_id=1050060
If bond connectivity is in the file then Jmol respects what
is in the file.
If no bond information is in the file then Jmol will apply a
general bonding algorithm.
Bonds constructed by Jmol are always single bonds.
PDB files rarely specify connectivity between atoms using
CONECT records.
For PDB files in particular it would be very difficult to
calculate bonding because there generally are no hydrogen
atoms.
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1221478&group_id=23629

Bugs item #1231370, was opened at 2005-07-02 01:18
Message generated for change (Comment added) made by migueljmol
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1231370&group_id=23629
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Won Kyu Park (wkpark)
Assigned to: Nobody/Anonymous (nobody)
Summary: Jmol rendering bug
Initial Comment:
Hello
I made a flash movie to show you this rendering bug
and this movie simply describe it.
when I zoom in a molecule with ball & sticks model
this problem is significant
All jmol versions have same problem
http://chemie.skku.ac.kr/~wkpark/demos/jmolbug.html
Regards,
W. K. Park
----------------------------------------------------------------------
>Comment By: Miguel (migueljmol)
Date: 2005-07-28 12:38
Message:
Logged In: YES
user_id=1050060
This is a known problem that occurs when you zoom in close
and have perspective depth turned on.
I tried to avoid the problem by not allowing people to zoom
in so much.
But many people complained and said that they needed to zoom
in further.
You can avoid the problem if you say
'set perspectiveDepth off'
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1231370&group_id=23629

Bugs item #1240913, was opened at 2005-07-19 11:10
Message generated for change (Comment added) made by migueljmol
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1240913&group_id=23629
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: Application
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: setting shapes using source libraries
Initial Comment:
I had a simple question about using the JmolViewer as a
development tool kit that can be integrated into other
Java applications.
I am using the examples from CVS to integrate into my
viewer application. I was wondering what methods I can
call to set shapes? to ribbon or meshed ribbon for
example.
I have the source and am using the Viewer object in my
Viewer JmolPanel window. Making the setShapeSize(int,
int) public and calling that does not work as Frame in
modelManager == null.
How would I use custom shapes?
Thank you and sorry for the dumb question.
----------------------------------------------------------------------
>Comment By: Miguel (migueljmol)
Date: 2005-07-28 12:30
Message:
Logged In: YES
user_id=1050060
I do not understand the question.
And I do not know how to get in touch with you since this
was submitted by 'anonymous' and I do not have your email.
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1240913&group_id=23629

Bugs item #1155968, was opened at 2005-03-03 11:15
Message generated for change (Comment added) made by migueljmol
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1155968&group_id=23629
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: File Input/Output
Group: None
>Status: Closed
>Resolution: Invalid
Priority: 5
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Miguel (migueljmol)
Summary: Jmol gets confused by GAMESS output file
Initial Comment:
When opening the attached file with Jmol v.10.00.11, no
bonds are shown, the oxygens are shown as Xx atoms
(small and pink instead of medium red atoms) and
calcium atoms are mistaken as carbons.
The Jmol console does not report any errors.
Jmol v.9 identifies correctly all the atoms and bonds.
The attached output file is the smallest case I found
where this bug shows up. Maybe it has something to do
with the high symmetry (Td group) of the molecule?
The attached GAMESS output file should NOT be
redistributed. I am submitting it for debugging only.
Thanx for your attention.
Victor M. Rosas Garcia
quimico69@...
----------------------------------------------------------------------
>Comment By: Miguel (migueljmol)
Date: 2005-07-28 12:29
Message:
Logged In: YES
user_id=1050060
The GAMESS output file that you sent me contains atoms
identified by 'CA',
'C', and '0'.
'CA' is recognized as calcium
'C' is recognized as carbon
'0' is not recognized ... because the character in the
GAMESS output file
is the digit zero, not the alphabetic letter 'O' ... 0 != O
(it is sad ... but also funny :-)
I edited the file and changed appropriate characters from
'0' -> 'O' ...
Jmol loads it fine.
I do not know anything about GAMESS or the process that was
used to
generate this file ... so I cannot tell you whether the
problem is in
GAMESS itself or was part of your input to GAMESS.
Miguel
----------------------------------------------------------------------
Comment By: Nobody/Anonymous (nobody)
Date: 2005-07-27 10:48
Message:
Logged In: NO
Jmol v.10.00.24 now correctly identifies de Calcium atoms,
but the oxygens are still shown as Xx atoms.
Thanx for your attention.
Victor M. Rosas Garcia
quimico69@...
----------------------------------------------------------------------
Comment By: Miguel (migueljmol)
Date: 2005-03-03 11:53
Message:
Logged In: YES
user_id=1050060
The GAMESS reader was completely rewritten between Jmol v9
and Jmol v10 ... like all the other code.
Probably some type of column-alignment problem ... hence Ca
-> C ... but that does not explain the problem with O
There are no bonds because the element Xx (unknown) does not
bond.
There was no attached file ... can you send it to me off-list?
Miguel
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1155968&group_id=23629

Victor wrote:
> Jmol v.10.00.24 now correctly identifies de Calcium atoms,
> but the oxygens are still shown as Xx atoms.
Victor,
The GAMESS output file that you sent me contains atoms identified by 'CA'=
,
'C', and '0'.
'CA' is recognized as calcium
'C' is recognized as carbon
'0' is not recognized ... because the character in the GAMESS output file=
is the digit zero, not the alphabetic letter 'O' ... 0 =21=3D O
(it is sad ... but also funny :-)
I edited the file and changed appropriate characters from '0' -> 'O' ...
Jmol loads it fine.
I do not know anything about GAMESS or the process that was used to
generate this file ... so I cannot tell you whether the problem is in
GAMESS itself or was part of your input to GAMESS.
Miguel

Bugs item #1155968, was opened at 2005-03-03 08:15
Message generated for change (Comment added) made by nobody
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1155968&group_id=23629
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: File Input/Output
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Miguel (migueljmol)
Summary: Jmol gets confused by GAMESS output file
Initial Comment:
When opening the attached file with Jmol v.10.00.11, no
bonds are shown, the oxygens are shown as Xx atoms
(small and pink instead of medium red atoms) and
calcium atoms are mistaken as carbons.
The Jmol console does not report any errors.
Jmol v.9 identifies correctly all the atoms and bonds.
The attached output file is the smallest case I found
where this bug shows up. Maybe it has something to do
with the high symmetry (Td group) of the molecule?
The attached GAMESS output file should NOT be
redistributed. I am submitting it for debugging only.
Thanx for your attention.
Victor M. Rosas Garcia
quimico69@...
----------------------------------------------------------------------
Comment By: Nobody/Anonymous (nobody)
Date: 2005-07-27 07:48
Message:
Logged In: NO
Jmol v.10.00.24 now correctly identifies de Calcium atoms,
but the oxygens are still shown as Xx atoms.
Thanx for your attention.
Victor M. Rosas Garcia
quimico69@...
----------------------------------------------------------------------
Comment By: Miguel (migueljmol)
Date: 2005-03-03 08:53
Message:
Logged In: YES
user_id=1050060
The GAMESS reader was completely rewritten between Jmol v9
and Jmol v10 ... like all the other code.
Probably some type of column-alignment problem ... hence Ca
-> C ... but that does not explain the problem with O
There are no bonds because the element Xx (unknown) does not
bond.
There was no attached file ... can you send it to me off-list?
Miguel
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1155968&group_id=23629

Nico wrote:
>>Q: What is the JmolProcessor?
>
> I think it's the extension that enables embedding Jmol applets in wikis=
.
> For what I understand in http://wiki.jmol.org/JmolProcessor, there is
> already one done for MoinMoin wiki, and it is available in Jmol wiki.
I did not know that this already existed.
I built a different one for Moin. The usage closely mimics the Jmol.js
library.
Q: Who built the Moin JmolProcessor? Oliver?
Miguel
-----
Open Source Molecular Visualization
http://www.jmol.org
miguel=40jmol.org
-----

>De: =22Miguel=22 <miguel=40jmol.org>
>
>Oliver,
>
>I am interested in extending MoinMoin so that we can embed JmolApplets +
>controls directly into the wiki pages.
>
=2E..
>
>
>Oliver wrote:
>> I've just updated the JmolWiki to Moin-1.3.0. It was easier than I've
>> expected. Even the JmolProcessor still works. :-)
>
>Q: What is the JmolProcessor?
I think it's the extension that enables embedding Jmol applets in wikis.
For what I understand in http://wiki.jmol.org/JmolProcessor, there is alre=
ady one done for MoinMoin wiki, and it is available in Jmol wiki.
Nicolas

HI
I am trying to load different models into same applet. I want to know
if there is a way to know if the javascript completed. I mean to say,
that I can see the message on the status bar like" jmol script
executing" and "jmol script completed". Is there way to capture "jmol
script completed", so that I can fire an event based on it.
http://eon.cm.utexas.edu/~alokvaid/jmol/test8.php
( I am using 2 swaping divs to load 2 models at same time, and load
the next model in hidden div)
regards
Alok Vaid
Chemistry Dept.
UT Austin

Oliver,
I am interested in extending MoinMoin so that we can embed JmolApplets +
controls directly into the wiki pages.
It seems to me that the macro mechanism can easily be used to add the
controls.
It would be best if the macros in the body output JavaScript calls into
the Jmol.js library.
I do not know how to extend MoinMoin so that it will include a .js file u=
p
in the <HEAD> section.
Q: Is this something you could help me with?
Oliver wrote:
> I've just updated the JmolWiki to Moin-1.3.0. It was easier than I've
> expected. Even the JmolProcessor still works. :-)
Q: What is the JmolProcessor?
Miguel
-----
Open Source Molecular Visualization
http://www.jmol.org
miguel=40jmol.org
-----

Feature Requests item #1245360, was opened at 2005-07-26 17:13
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1245360&group_id=23629
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: Interface Improvements
Group: None
Status: Open
Priority: 5
Submitted By: Andrew Milsted (bluerhinos)
Assigned to: Nobody/Anonymous (nobody)
Summary: Viewing in Stereo (with red/green glasses)
Initial Comment:
Hi
I am using jmol in a educational website showing how moleclues are
in 3d, and was wondering, to add interactivity for the kids, if jmol can
produce this kind of stereo images.
If not can i make it a feature request.
Andrew Milsted
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1245360&group_id=23629

>>I cannot find any references to this page from the current web site.
>>
>>The page should probably be deleted at this point, but I want to know
>>whether or not there are existing references to it.
>
> I think Angel reported the same problem when doing the Spanish translat=
ion
> of the website. I asked him the same question and if I remember correct=
ly
> he told me about a link on the wiki.
> I don't have access to my personal computer this week, so I can't check=
> for sure.
I found the reference on the Wiki and deleted it.
I am going to remove this subdirectory from the Jmol-web project. We can
retrieve it from CVS if necessary.
Miguel
-----
Open Source Molecular Visualization
http://www.jmol.org
miguel=40jmol.org
-----

De: =22Miguel=22 <miguel=40jmol.org>
>
>> Just visited the http://jmol.sourceforge.net/applet/ page where lots of
>> structures didn't load.
>
>Robley,
>
>Q: How did you get to this page?
>
>This page applies to the previous version of Jmol ... version 9.
>
>Jmol version 10 supports a newer version of CML. That is why it did not l=
oad.
>
>I cannot find any references to this page from the current web site.
>
>The page should probably be deleted at this point, but I want to know
>whether or not there are existing references to it.
I think Angel reported the same problem when doing the Spanish translation=
of the website. I asked him the same question and if I remember correctly=
he told me about a link on the wiki.
I don't have access to my personal computer this week, so I can't check fo=
r sure.
Nicolas

> Just visited the http://jmol.sourceforge.net/applet/ page where lots of=
> structures didn't load.
Robley,
Q: How did you get to this page?
This page applies to the previous version of Jmol ... version 9.
Jmol version 10 supports a newer version of CML. That is why it did not l=
oad.
I cannot find any references to this page from the current web site.
The page should probably be deleted at this point, but I want to know
whether or not there are existing references to it.
Miguel

On Jul 24, 2005, at 16:20 , Miguel wrote:
>>> Please write Jmol with a lower case 'm' to avoid confusion with
>>> other
>>> projects.
>>>
>> Sorry about the misspelling - will write Jmol from now on.
>>
>
> No problem
>
>
>>> model all
>>>
>> Thanks - I didn't realize that was available.
>>
>
> Well, that is not surprising given the state of our documentation.
>
>
>>> Q: Please confirm that what you are asking for is the ability to
>>> add an
>>> additional model into the currently loaded file ... it would be
>>> exactly
>>> the same coordinate system, center, etc.
>>>
>> That would be perfect (it would be identical to loading an NMR
>> ensemble but one model at a time rather than all in the same PDB
>> file).
>>
>
> OK
>
> This is not easily done ... and it will not happen in the near future.
>
> But I recently received a similar request and I wanted to clarify
> that it
> was more-or-less the same.
Definitely understand (for now, I have a client side script that
builds up a multi-model PDB file in a string and passes it to Jmol so
there's no rush (will just make our Javascript a bit cleaner)).
Scott
> Miguel
>
> -----
> Open Source Molecular Visualization
> http://www.jmol.org
> miguel@...
> -----
>
>

>> Please write Jmol with a lower case 'm' to avoid confusion with other
>> projects.
> Sorry about the misspelling - will write Jmol from now on.
No problem
>> model all
> Thanks - I didn't realize that was available.
Well, that is not surprising given the state of our documentation.
>> Q: Please confirm that what you are asking for is the ability to
>> add an
>> additional model into the currently loaded file ... it would be
>> exactly
>> the same coordinate system, center, etc.
> That would be perfect (it would be identical to loading an NMR
> ensemble but one model at a time rather than all in the same PDB file).=
OK
This is not easily done ... and it will not happen in the near future.
But I recently received a similar request and I wanted to clarify that it=
was more-or-less the same.
Miguel
-----
Open Source Molecular Visualization
http://www.jmol.org
miguel=40jmol.org
-----

On Jul 24, 2005, at 15:17 , Miguel wrote:
> Scott wrote:
>
>> I'm currently working on a web application using JMol.
>>
>
> Please write Jmol with a lower case 'm' to avoid confusion with other
> projects.
Sorry about the misspelling - will write Jmol from now on.
>
>> We have already implemented part of our site using JMol ( http://
>> flexweb.la.asu.edu/software/first/first_online/ ; free registration
>> required).
>>
>> Overall, we've found JMol to be a great improvement over Chime but
>> there are two features that we could really use that don't seem to be
>> available yet.
>>
>> First, one of our applications requires overlaying structures or
>> models (as with the enclosed figure).
>>
>
> If I understand you correctly, you would like to display multiple
> models
> at this same time. Jmol currently supports this through the script
> command:
>
> model all
Thanks - I didn't realize that was available.
>
>> It would also be nice (though not essential) if there were a way to
>> append a structure as a new model in an existing set of models. Our
>> application would involve a simulation on a server that generates a
>> set of models. A client-side script would periodically grab a new
>> model and tell JMol to append the new model to an existing set.
>>
>
> Q: Please confirm that what you are asking for is the ability to
> add an
> additional model into the currently loaded file ... it would be
> exactly
> the same coordinate system, center, etc.
That would be perfect (it would be identical to loading an NMR
ensemble but one model at a time rather than all in the same PDB file).
Thanks, again,
Scott
>
> Miguel
>
>

Scott wrote:
> I'm currently working on a web application using JMol.
Please write Jmol with a lower case 'm' to avoid confusion with other
projects.
> We have already implemented part of our site using JMol ( http://
> flexweb.la.asu.edu/software/first/first_online/ ; free registration
> required).
>
> Overall, we've found JMol to be a great improvement over Chime but
> there are two features that we could really use that don't seem to be
> available yet.
>
> First, one of our applications requires overlaying structures or
> models (as with the enclosed figure).
If I understand you correctly, you would like to display multiple models
at this same time. Jmol currently supports this through the script
command:
model all
> It would also be nice (though not essential) if there were a way to
> append a structure as a new model in an existing set of models. Our
> application would involve a simulation on a server that generates a
> set of models. A client-side script would periodically grab a new
> model and tell JMol to append the new model to an existing set.
Q: Please confirm that what you are asking for is the ability to add an
additional model into the currently loaded file ... it would be exactly
the same coordinate system, center, etc.
Miguel

Hi,
I believe that if you read a structure file with more than one set of=20
atoms (molecules, structures or frames), you should be able to show all=20=
sets by issuing the command
'frame 0'
in the script window.
I am not familiar enough with the pdb file format to know whether it=20
allows one to define more than more than one, but xyz file formats and=20=
such do allow that.
Cheers,
Ren=E9
PS the name is Jmol not JMol (JMol is a different application).
On Jul 24, 2005, at 4:15 PM, Scott Menor wrote:
> Hello,
>
> I'm currently working on a web application using JMol.
>
> We have already implemented part of our site using JMol (=20
> http://flexweb.la.asu.edu/software/first/first_online/ ; free=20
> registration required).
>
> Overall, we've found JMol to be a great improvement over Chime but=20
> there are two features that we could really use that don't seem to be=20=
> available yet.
>
> First, one of our applications requires overlaying structures or=20
> models (as with the enclosed figure).
>
> It would also be nice (though not essential) if there were a way to=20
> append a structure as a new model in an existing set of models. Our=20
> application would involve a simulation on a server that generates a=20
> set of models. A client-side script would periodically grab a new=20
> model and tell JMol to append the new model to an existing set.
> <flexibilityBackboneOverlay.small.png>
> Thanks,
> Scott